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Trypsin Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
Trypsin (EC 22.214.171.124) is a serine protease from the PA clan superfamily, found in the digestive system of many vertebrates, where it hydrolyses proteins. Trypsin is produced in the pancreas as the inactive protease trypsinogen. Trypsin cleaves peptide chains mainly at the carboxyl side of the amino acids lysine or arginine, except when either is followed by proline. It is used for numerous biotechnological processes. The process is commonly referred to as trypsin proteolysis or trypsinisation, and proteins that have been digested/treated with trypsin are said to have been trypsinized.
In the duodenum, trypsin catalyzes the hydrolysis of peptide bonds, breaking down proteins into smaller peptides. The peptide products are then further hydrolyzed into amino acids via other proteases, rendering them available for absorption into the blood stream. Tryptic digestion is a necessary step in protein absorption as proteins are generally too large to be absorbed through the lining of the small intestine.
Trypsin is produced as the inactive zymogen trypsinogen in the pancreas. When the pancreas is stimulated by cholecystokinin, it is then secreted into the first part of the small intestine (the duodenum) via the pancreatic duct. Once in the small intestine, the enzyme enteropeptidase activates trypsinogen into trypsin by proteolytic cleavage. Auto catalysis can happen with trypsin using trypsinogen as the substrate. This activation mechanism is common for most serine proteases, and serves to prevent autodegradation of the pancreas.
The enzymatic mechanism is similar to that of other serine proteases. These enzymes contain a catalytic triad consisting of histidine-57, aspartate-102, and serine-195. These three residues form a charge relay that increases nucleophilicity of the active site serine. This is achieved by modifying the electrostatic environment of the serine. The enzymatic reaction that trypsin catalyzes is thermodynamically favorable but requires significant activation energy (it is "kinetically unfavorable"). In addition, trypsin contains an "oxyanion hole" formed by the backbone amide hydrogen atoms of Gly-193 and Ser-195, which serves to stabilize the developing negative charge on the carbonyl oxygen atom of the cleaved amides.
The aspartate residue (Asp 189) located in the catalytic pocket (S1) of trypsin is responsible for attracting and stabilizing positively charged lysine and/or arginine, and is, thus, responsible for the specificity of the enzyme. This means that trypsin predominantly cleaves proteins at the carboxyl side (or "C-terminal side") of the amino acids lysine and arginine except when either is bound to a C-terminal proline, although large-scale mass spectrometry data suggest cleavage occurs even with proline. Trypsin is considered an endopeptidase, i.e., the cleavage occurs within the polypeptide chain rather than at the terminal amino acids located at the ends of polypeptides.
As a protein trypsin has various molecular weights depending on the source. For example, a molecular weight of 23.3 kDa is reported for trypsin from bovine and porcine sources.
The activity of trypsin is not affected by the enzyme inhibitor tosyl phenylalanyl chloromethyl ketone, TPCK, which deactivates chymotrypsin. This is important because, in some applications, like mass spectrometry, the specificity of cleavage is important.
Trypsin should be stored at very cold temperatures (between −20°C and −80°C) to prevent autolysis, which may also be impeded by storage of trypsin at pH 3 or by using trypsin modified by reductive methylation. When the pH is adjusted back to pH 8, activity returns.
The following human genes encode proteins with trypsin enzymatic activity:
Other isoforms of trypsin may also be found in other organisms.
Activation of trypsin from proteolytic cleavage of trypsinogen in the pancreas can lead to a series of events that cause pancreatic self-digestion, resulting in pancreatitis. One consequence of the autosomal recessive disease cystic fibrosis is a deficiency in transport of trypsin and other digestive enzymes from the pancreas. This leads to the disorder termed meconium ileus. This disorder involves intestinal obstruction (ileus) due to overly thick meconium, which is normally broken down by trypsin and other proteases, then passed in feces.
Trypsin is available in high quantity in pancreases, and can be purified rather easily. Hence it has been used widely in various biotechnological processes.
In a tissue culture lab, trypsin is used to re-suspend cells adherent to the cell culture dish wall during the process of harvesting cells. Some cell types have a tendency to "stick" - or adhere - to the sides and bottom of a dish when cultivated in vitro. Trypsin is used to cleave proteins bonding the cultured cells to the dish, so that the cells can be suspended in fresh solution and transferred to fresh dishes.
Trypsin can also be used to dissociate dissected cells (for example, prior to cell fixing and sorting).
Trypsin can be used to break down casein in breast milk. If trypsin is added to a solution of milk powder, the breakdown of casein will cause the milk to become translucent. The rate of reaction can be measured by using the amount of time it takes for the milk to turn translucent.
Trypsin is commonly used in biological research during proteomics experiments to digest proteins into peptides for mass spectrometry analysis, e.g. in-gel digestion. Trypsin is particularly suited for this, since it has a very well defined specificity, as it hydrolyzes only the peptide bonds in which the carbonyl group is contributed either by an Arg or Lys residue.
Trypsin can also be used to dissolve blood clots in its microbial form and treat inflammation in its pancreatic form.
Commercial protease preparations usually consist of a mixture of various protease enzymes that often includes trypsin. These preparations are widely utilized in food processing:
- as a baking enzyme to improve the workability of dough;
- in the extraction of seasonings and flavourings from vegetable or animal proteins and in the manufacture of sauces;
- to control aroma formation in cheese and milk products;
- to improve the texture of fish products;
- to tenderize meat;
- during cold stabilization of beer;
- in the production of hypoallergenic food where proteases break down specific allergenic proteins into nonallergenic peptides. For example, proteases are used to produce hypoallergenic baby food from cow’s milk thereby diminishing the risk of babies developing milk allergies.
In order to prevent the action of active trypsin in the pancreas which can be highly damaging, inhibitors such as BPTI and SPINK1 in the pancreas and α1-antitrypsin in the serum are present as part of the defense against its inappropriate activation. Any trypsin prematurely formed from the inactive trypsinogen would be bound by the inhibitor. The protein-protein interaction between trypsin and its inhibitors is one of the tightest found, and trypsin is bound by some of its pancreatic inhibitors essentially irreversibly. In contrast with nearly all known protein assemblies, some complexes of trypsin bound by its inhibitors do not readily dissociate after treatment with 8M urea.
- "Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements". Protein Sci. 13 (4): 1056–70. doi:10.1110/ps.03498604. PMC 2280040. PMID 15044735.; Leiros HK, Brandsdal BO, Andersen OA, Os V, Leiros I, Helland R, Otlewski J, Willassen NP, Smalås AO (April 2004).
- Rawlings ND, Barrett AJ (1994). "Families of serine peptidases". Meth. Enzymol. Methods in Enzymology 244: 19–61. doi:10.1016/0076-6879(94)44004-2. ISBN 978-0-12-182145-6. PMID 7845208.
- The German physiologist Wilhelm Kühne (1837-1900) discovered trypsin in 1876. See: W. Kühne (1877) "Über das Trypsin (Enzym des Pankreas)", Verhandlungen des naturhistorisch-medicinischen Vereins zu Heidelberg, new series, vol. 1, no. 3, pages 194-198.
- Polgár L (October 2005). "The catalytic triad of serine peptidases". Cell. Mol. Life Sci. 62 (19–20): 2161–72. doi:10.1007/s00018-005-5160-x. PMID 16003488.
- "Sequencing Grade Modified Trypsin" (PDF). www.promega.com. 2007-04-01. Retrieved 2009-02-08.
- Rodriguez J, Gupta N, Smith RD, Pevzner PA (2008). "Does trypsin cut before proline?". J. Proteome Res. 7 (1): 300–305. doi:10.1021/pr0705035. PMID 18067249.
- Noone PG, Zhou Z, Silverman LM, Jowell PS, Knowles MR, Cohn JA (December 2001). "Cystic fibrosis gene mutations and pancreatitis risk: relation to epithelial ion transport and trypsin inhibitor gene mutations". Gastroenterology 121 (6): 1310–9. doi:10.1053/gast.2001.29673. PMID 11729110.
- "Trypsin-EDTA (0.25%)". Stem Cell Technologies. Retrieved 2012-02-23.
- "Protease - GMO Database". GMO Compass. European Union. 2010-07-10. Retrieved 2012-01-01.
- Voet & Voet (1995). Biochemisty (2nd ed.). John Wiley & Sons. pp. 396–400. ISBN 0-471-58651-X.
- N. Levilliers, M. Péron, B. Arrio, J. Pudles (October 1970). "On the mechanism of action of proteolyticinhibitors: IV. Effect of 8murea on the stability of trypsin in trypsin-lnhibitor complexes". Archives of Biochemistry and Biophysics 140 (2): 474–483. doi:10.1016/0003-9861(70)90091-3. PMID 5528741.
- The MEROPS online database for peptidases and their inhibitors: Trypsin 1 S01.151, Trypsin 2 S01.258, Trypsin 3 S01.174
- Trypsin Inhibitors and Trypsin Assay Method at Sigma-Aldrich
- Trypsin at the US National Library of Medicine Medical Subject Headings (MeSH)
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Trypsin Provide feedback
No Pfam abstract.
Sprang S, Standing T, Fletterick RJ, Stroud RM, Finer-Moore J, Xuong NH, Hamlin R, Rutter WJ, Craik CS; , Science 1987;237:905-909.: The Three Dimensional Structure of Asnl02 Trypsin: Role of Aspl02 in Serine Protease Catalysis PUBMED:3112942 EPMC:3112942
Internal database links
|SCOOP:||Peptidase_C3 Peptidase_S3 Pico_P2A Peptidase_S7 DUF31 Peptidase_S6 Peptidase_S29 DUF316 Peptidase_S32 Peptidase_S55 DUF1986 Peptidase_S46 Trypsin_2|
|Similarity to PfamA using HHSearch:||DUF316 DUF1986 Trypsin_2|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001254
This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S)).
The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum [PUBMED:7845208]. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules [PUBMED:7845208].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||serine-type endopeptidase activity (GO:0004252)|
|Biological process||proteolysis (GO:0006508)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
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EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This clan contains a diverse set of peptidases with the trypsin fold.
The clan contains the following 24 members:DUF1986 DUF31 DUF316 Peptidase_C24 Peptidase_C3 Peptidase_C30 Peptidase_C37 Peptidase_C3G Peptidase_C4 Peptidase_C62 Peptidase_S29 Peptidase_S3 Peptidase_S30 Peptidase_S31 Peptidase_S32 Peptidase_S39 Peptidase_S46 Peptidase_S55 Peptidase_S6 Peptidase_S7 Peptidase_S76 Pico_P2A Trypsin Trypsin_2
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||SCOP and Prosite|
|Author:||Lutfiyya LL, Sonnhammer ELL|
|Number in seed:||71|
|Number in full:||17288|
|Average length of the domain:||208.20 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||56.84 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||23|
|Download:||download the raw HMM for this family|
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There are 67 interactions for this family. More...
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Trypsin domain has been found. There are 2333 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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